PSAMM: A Portable System for the Analysis of Metabolic Models
Fig 5
A diagram illustrating the modular representation of model components in the YAML format.
The data structure is divided into the static components of model annotation (A) and the dynamic components of simulation settings (B). The reaction and compound annotation databases are associated with a number of required (highlighted in black, e.g. “- id” and “- equation” for reactions) and optional (gray) data entries, and user-defined, model-specific data entries are permitted in the annotation databases. The simulation settings can be represented with various combinations of the model, limits, and media files. Alternative conditions may be defined using a number of alternative modules that can be switched with one another.